The spam filter influences the number of times a comment needs to be flagged before it becomes [flagged] and gets killed, but if it says [flagged], someone used the "flag" button at least once. Sometimes just downvoting a spam comment is enough to kill it; those just get marked [dead] and not [flagged].
I don't believe that's the case. HN is running some kind of automated slop detector that classifies any suspected LLM output as "slop" even if it's entirely in-context for the conversation (e.g., a conversation about LLM output.) The comment gets autoflagged the moment it's posted. This has been the case for a while now, I've run afoul of it myself.
It sucks, and I can only imagine they implemented it because they felt they had no other option to deal with the onslaught of bots that's appeared lately.
One thing they could do to improve the situation is to weight vouching heavily by karma. I have plenty of karma but I don't think I've ever successfully pulled a comment out of the [dead] state by vouching for it. Legitimate comments that get flagged by mistake tend to stay that way for the duration of the discussion.
Comments that get autokilled are just [dead], not [flagged] [dead]. If you cannot vouch comments back to life, it's also possible that your vouching privileges were taken away because the mods disagreed with your vouching decisions. When you see something really great that is [dead] and vouching doesn't help, you can try emailing the mods and mention that vouching didn't work. If it's actually great, maybe they'll let you vouch again. (Happened to me.)